BN1722 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 5 6.7425e-05 1.3100e-03
Layer 3 1.0220e-04 2.0704e-03
Layer 4 2.0346e-04 1.1561e-03
Layer 6 5.3490e-04 3.2254e-03
WM 8.5048e-04 2.9198e-01
Layer 2 3.2144e-03 9.6976e-02
Layer 1 3.1140e-01 4.2842e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 5 2.4941 0.7259
STMN2 Layer 5 2.6924 0.7111
KLC1 Layer 4 2.4912 0.7081
MORF4L1 Layer 5 2.6660 0.7049
STXBP1 Layer 4 2.6924 0.7009
NDRG4 Layer 5 2.5059 0.7009
BASP1 Layer 5 2.3926 0.7007
RTN1 Layer 4 2.6484 0.7000
ENO2 Layer 4 2.8770 0.6991
NORAD Layer 4 2.2363 0.6965
SERINC1 Layer 5 2.4941 0.6953
PFN2 Layer 4 2.9336 0.6945
SH3GL2 Layer 5 2.5029 0.6905
SNRPN Layer 4 2.4883 0.6895
SYN2 Layer 4 2.5693 0.6869
TUBB2A Layer 5 2.6133 0.6868
FXYD6 Layer 5 2.7012 0.6866
DPYSL2 Layer 5 2.4180 0.6866
ARL6IP1 Layer 5 2.3896 0.6865
CHCHD2 Layer 4 2.3398 0.6857
RAB6A Layer 5 2.1445 0.6852
GDI1 Layer 4 2.4180 0.6845
ATP5F1B Layer 4 2.6191 0.6839
TUBB3 Layer 5 2.2715 0.6839
EEF1A2 Layer 5 2.4697 0.6834
RTN3 Layer 4 2.4668 0.6825
DYNLRB1 Layer 4 2.5088 0.6824
NAPB Layer 5 2.3496 0.6822
PFKP Layer 4 2.8867 0.6807
STMN1 Layer 5 2.4844 0.6779
CABP1 Layer 5 2.3838 0.6768
ATP6V1B2 Layer 5 2.2676 0.6759
SNCG Layer 5 3.0391 0.6758
TUBB Layer 5 2.3105 0.6757
YWHAG Layer 5 2.5898 0.6752
ATP2B2 Layer 4 2.3965 0.6735
LDHA Layer 5 2.3594 0.6729
GAP43 Layer 5 2.5898 0.6728
PSAP Layer 4 2.3281 0.6727
NEFL Layer 3 2.5215 0.6723
AP2M1 Layer 5 2.6250 0.6722
TTC9B Layer 5 2.6133 0.6696
DCLK1 Layer 5 2.7188 0.6695
MORF4L2 Layer 4 2.6543 0.6692
SYT4 Layer 4 2.3184 0.6692
PPP2R1A Layer 5 2.3340 0.6692
TSPAN7 Layer 4 2.3848 0.6688
CLTA Layer 5 2.2168 0.6682
GNB1 Layer 4 2.3496 0.6681
CHGA Layer 4 2.6455 0.6680

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1722
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1722_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1722/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1722/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1722/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1722/report/PD/BN1722_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1722/report/PD/BN1722_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 05:55:59
  • Number of Processes: 10
  • Spending Time: 0h 3m